[gmx-users] Thanks to the developers heroic efforts!

[Szilárd Páll]

On Mon, Jun 30, 2014 at 4:52 PM, Mirco Wahab
<mirco.wahab at chemie.tu-freiberg.de> wrote:
> I installed 5.0 on both Linux (GPU) and Windows (GPU)
> and it seems to work very good.
>
> Some remarks:
> On 29.06.2014 22:53, Mark Abraham wrote:
>>
>> * The native GPU port available in GROMACS 4.6 supports a wider range of
>> simulation types, and now requires CUDA 4.0
>
>
> Should I read this 4.6 as 5.0?
>
>> * GROMACS tools are now bundled together into *just two binaries* - mdrun
>> and gmx. The latter contains most of the tools familiar to you, perhaps
>> with new names, and a couple of new ones. For the time being, the install
>> procedure will also create symbolic links so that your old scripts will
>> keep working for a time, but these will go away at some future point!
>
>
> Here on Linux, mdrun is a symlink to gmx, so there should be one binary?
> On Windows, there is only one exe file 'gmx.exe' and (by default)
> nothing else (no symlinks). So, on my systems, there is one binary
> executeable per system installation.

Indeed, in most cases there is only one binary, gmx; what the above
meant is that in total two binaries *can be* built gmx and mdrun.
While gmx always contains the mdrun tool, it is often useful to build
only mdrun e.g. for cluster compute-nodes with custom parallelization
options, e.g. MPI.

>> * There is support for the new TNG compressed trajectory format
>
>
> And, the usual default compressed trajectory is now named
> 'traj_comp.xtc'instead of 'traj.xtc', but 'traj.xtc' is still
> present. Maybe some people have to alter their shell scripts ;)
>
>> * GROMACS supports some special interactions for coarse-grained
>> interactions with Martini force fields
>
>
> Is this documented somewhere? I couldn't find it in the
> 5.0-manual.
>
>> * GROMACS support for Interactive Molecular Dynamics (IMD)
>
>
> This, I think, is cool! Thumbs up for this (I'm still
> figuring out how it works ...)
>
> (unfortunaletly, the solution of the gtest problem on VS2012
> didn't make it into the release - but the solution is easy to
> explain for people who want to build the native windows
> executeables.)
>
>
> Thank you very much!
>
> Regards
>
> M.
>
>
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